The growth of phytoplankton as well as crucial phytoplankton–bacteria interactions can be distorted by fungal parasites, with unknown regulatory mechanisms on a molecular level. To resolve those mechanisms, we will use OMICS on two model pathosystems. The 1^st phytoplankton–fungal parasite system is maintained in our laboratory and its genome has been sequenced in our ongoing work. It will thus allow us to conduct in-depth metagenomic and transcriptomic profiling during fungal parasitism. The 2^nd system is novel, as it has been isolated by our group very recently from the coastal ocean. We aim to reconstruct the draft genome of this first marine model system of its kind, to initiate future in-depth studies of parasitism in microbial communities. Our overarching question is: How do parasitic (fungal) infections on phytoplankton modulate functional and metabolic capacities, as well as gene expression patterns within phytoplankton–fungi–bacteria associations in aquatic environments?